@jbrowse/plugin-linear-genome-view 2.1.4 → 2.1.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (92) hide show
  1. package/dist/BaseLinearDisplay/components/BlockMsg.d.ts +9 -0
  2. package/dist/BaseLinearDisplay/components/BlockMsg.js +22 -0
  3. package/dist/BaseLinearDisplay/components/BlockMsg.js.map +1 -0
  4. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +5 -42
  5. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js.map +1 -1
  6. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +2 -5
  7. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +3 -20
  8. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
  9. package/dist/BaseLinearDisplay/models/TooLargeMessage.d.ts +11 -0
  10. package/dist/BaseLinearDisplay/models/TooLargeMessage.js +22 -0
  11. package/dist/BaseLinearDisplay/models/TooLargeMessage.js.map +1 -0
  12. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +1 -1
  13. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
  14. package/dist/LinearBareDisplay/model.d.ts +1 -1
  15. package/dist/LinearBasicDisplay/model.d.ts +1 -1
  16. package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts +4 -2
  17. package/dist/LinearGenomeView/components/Header.d.ts +1 -1
  18. package/dist/LinearGenomeView/components/Header.js +2 -2
  19. package/dist/LinearGenomeView/components/Header.js.map +1 -1
  20. package/dist/LinearGenomeView/components/LinearGenomeView.js +9 -10
  21. package/dist/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
  22. package/dist/LinearGenomeView/components/MiniControls.d.ts +1 -1
  23. package/dist/LinearGenomeView/components/MiniControls.js +13 -12
  24. package/dist/LinearGenomeView/components/MiniControls.js.map +1 -1
  25. package/dist/LinearGenomeView/components/SequenceSearchDialog.d.ts +4 -2
  26. package/dist/LinearGenomeView/components/SequenceSearchDialog.js.map +1 -1
  27. package/dist/LinearGenomeView/components/TrackLabel.js +4 -5
  28. package/dist/LinearGenomeView/components/TrackLabel.js.map +1 -1
  29. package/dist/LinearGenomeView/components/TracksContainer.d.ts +2 -3
  30. package/dist/LinearGenomeView/components/TracksContainer.js +1 -0
  31. package/dist/LinearGenomeView/components/TracksContainer.js.map +1 -1
  32. package/dist/LinearGenomeView/index.d.ts +8 -3
  33. package/dist/LinearGenomeView/index.js +47 -28
  34. package/dist/LinearGenomeView/index.js.map +1 -1
  35. package/dist/index.d.ts +1246 -3
  36. package/dist/index.js +3 -0
  37. package/dist/index.js.map +1 -1
  38. package/esm/BaseLinearDisplay/components/BlockMsg.d.ts +9 -0
  39. package/esm/BaseLinearDisplay/components/BlockMsg.js +16 -0
  40. package/esm/BaseLinearDisplay/components/BlockMsg.js.map +1 -0
  41. package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +6 -43
  42. package/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js.map +1 -1
  43. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +2 -5
  44. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js +3 -20
  45. package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
  46. package/esm/BaseLinearDisplay/models/TooLargeMessage.d.ts +11 -0
  47. package/esm/BaseLinearDisplay/models/TooLargeMessage.js +17 -0
  48. package/esm/BaseLinearDisplay/models/TooLargeMessage.js.map +1 -0
  49. package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts +1 -1
  50. package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
  51. package/esm/LinearBareDisplay/model.d.ts +1 -1
  52. package/esm/LinearBasicDisplay/model.d.ts +1 -1
  53. package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts +4 -2
  54. package/esm/LinearGenomeView/components/Header.d.ts +1 -1
  55. package/esm/LinearGenomeView/components/Header.js +2 -2
  56. package/esm/LinearGenomeView/components/Header.js.map +1 -1
  57. package/esm/LinearGenomeView/components/LinearGenomeView.js +9 -10
  58. package/esm/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
  59. package/esm/LinearGenomeView/components/MiniControls.d.ts +1 -1
  60. package/esm/LinearGenomeView/components/MiniControls.js +13 -12
  61. package/esm/LinearGenomeView/components/MiniControls.js.map +1 -1
  62. package/esm/LinearGenomeView/components/SequenceSearchDialog.d.ts +4 -2
  63. package/esm/LinearGenomeView/components/SequenceSearchDialog.js.map +1 -1
  64. package/esm/LinearGenomeView/components/TrackLabel.js +4 -5
  65. package/esm/LinearGenomeView/components/TrackLabel.js.map +1 -1
  66. package/esm/LinearGenomeView/components/TracksContainer.d.ts +2 -3
  67. package/esm/LinearGenomeView/components/TracksContainer.js +1 -0
  68. package/esm/LinearGenomeView/components/TracksContainer.js.map +1 -1
  69. package/esm/LinearGenomeView/index.d.ts +8 -3
  70. package/esm/LinearGenomeView/index.js +44 -27
  71. package/esm/LinearGenomeView/index.js.map +1 -1
  72. package/esm/index.d.ts +1246 -3
  73. package/esm/index.js +4 -1
  74. package/esm/index.js.map +1 -1
  75. package/package.json +3 -2
  76. package/src/BaseLinearDisplay/components/BlockMsg.tsx +42 -0
  77. package/src/BaseLinearDisplay/components/ServerSideRenderedBlockContent.tsx +16 -91
  78. package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +3 -31
  79. package/src/BaseLinearDisplay/models/TooLargeMessage.tsx +34 -0
  80. package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +2 -2
  81. package/src/LinearGenomeView/components/ExportSvgDialog.tsx +2 -2
  82. package/src/LinearGenomeView/components/Header.tsx +8 -6
  83. package/src/LinearGenomeView/components/{LinearGenomeView.test.js → LinearGenomeView.test.tsx} +16 -7
  84. package/src/LinearGenomeView/components/LinearGenomeView.tsx +14 -17
  85. package/src/LinearGenomeView/components/MiniControls.tsx +39 -37
  86. package/src/LinearGenomeView/components/SequenceSearchDialog.tsx +1 -4
  87. package/src/LinearGenomeView/components/TrackLabel.tsx +6 -9
  88. package/src/LinearGenomeView/components/TracksContainer.tsx +3 -3
  89. package/src/LinearGenomeView/components/__snapshots__/{LinearGenomeView.test.js.snap → LinearGenomeView.test.tsx.snap} +32 -102
  90. package/src/LinearGenomeView/index.test.ts +2 -2
  91. package/src/LinearGenomeView/index.tsx +53 -28
  92. package/src/index.ts +5 -0
package/dist/LinearGenomeView/components/TrackLabel.js CHANGED
@@ -46,12 +46,11 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
46
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  }));
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  function getTrackName(track, session) {
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  const trackName = (0, configuration_1.getConf)(track, 'name');
49
- if ((0, configuration_1.getConf)(track, 'type') === 'ReferenceSequenceTrack') {
49
+ if (!trackName && (0, configuration_1.getConf)(track, 'type') === 'ReferenceSequenceTrack') {
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  const asm = session.assemblies.find(a => a.sequence === track.configuration);
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- return (trackName ||
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- (asm
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- ? `Reference Sequence (${(0, configuration_1.readConfObject)(asm, 'displayName') || (0, configuration_1.readConfObject)(asm, 'name')})`
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- : 'Reference Sequence'));
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+ return asm
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+ ? `Reference Sequence (${(0, configuration_1.readConfObject)(asm, 'displayName') || (0, configuration_1.readConfObject)(asm, 'name')})`
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+ : 'Reference Sequence';
55
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  }
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  return trackName;
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  }
package/dist/LinearGenomeView/components/TrackLabel.js.map CHANGED
@@ -1 +1 @@
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package/dist/LinearGenomeView/components/TracksContainer.d.ts CHANGED
@@ -1,7 +1,6 @@
1
1
  import React from 'react';
2
- import { Instance } from 'mobx-state-tree';
3
- import { LinearGenomeViewStateModel } from '..';
4
- declare type LGV = Instance<LinearGenomeViewStateModel>;
2
+ import { LinearGenomeViewModel } from '..';
3
+ declare type LGV = LinearGenomeViewModel;
5
4
  declare function TracksContainer({ children, model, }: {
6
5
  children: React.ReactNode;
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  model: LGV;
package/dist/LinearGenomeView/components/TracksContainer.js CHANGED
@@ -30,6 +30,7 @@ const react_1 = __importStar(require("react"));
30
30
  const mui_1 = require("tss-react/mui");
31
31
  const mobx_react_1 = require("mobx-react");
32
32
  const normalize_wheel_1 = __importDefault(require("normalize-wheel"));
33
+ // locals
33
34
  const __1 = require("..");
34
35
  const RubberBand_1 = __importDefault(require("./RubberBand"));
35
36
  const ScaleBar_1 = __importDefault(require("./ScaleBar"));
package/dist/LinearGenomeView/components/TracksContainer.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/LinearGenomeView/index.d.ts CHANGED
@@ -1,3 +1,4 @@
1
+ import React from 'react';
1
2
  import { Region } from '@jbrowse/core/util/types';
2
3
  import { MenuItem } from '@jbrowse/core/ui';
3
4
  import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
@@ -7,6 +8,8 @@ import PluginManager from '@jbrowse/core/PluginManager';
7
8
  import { renderToSvg } from './components/LinearGenomeViewSvg';
8
9
  import RefNameAutocomplete from './components/RefNameAutocomplete';
9
10
  import SearchBox from './components/SearchBox';
11
+ import ZoomControls from './components/ZoomControls';
12
+ import LinearGenomeView from './components/LinearGenomeView';
10
13
  export interface BpOffset {
11
14
  refName?: string;
12
15
  index: number;
@@ -91,6 +94,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
91
94
  readonly interRegionPaddingWidth: number;
92
95
  readonly assemblyNames: string[];
93
96
  } & {
97
+ MiniControlsComponent(): React.FC<any>;
98
+ HeaderComponent(): React.FC<any>;
94
99
  readonly assemblyErrors: string;
95
100
  readonly assembliesInitialized: boolean;
96
101
  readonly initialized: boolean;
@@ -171,6 +176,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
171
176
  showAllRegionsInAssembly(assemblyName?: string): void;
172
177
  setDraggingTrackId(idx?: string): void;
173
178
  setScaleFactor(factor: number): void;
179
+ clearView(): void;
180
+ exportSvg(opts?: ExportSvgOptions): Promise<void>;
174
181
  } & {
175
182
  slide: (viewWidths: number) => void;
176
183
  } & {
@@ -201,11 +208,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
201
208
  readonly visibleLocStrings: string;
202
209
  readonly coarseVisibleLocStrings: string;
203
210
  } & {
204
- clearView(): void;
205
211
  setCoarseDynamicBlocks(blocks: BlockSet): void;
206
212
  afterAttach(): void;
207
213
  } & {
208
- exportSvg(opts?: ExportSvgOptions): Promise<void>;
209
214
  /**
210
215
  * offset is the base-pair-offset in the displayed region, index is the index of the
211
216
  * displayed region in the linear genome view
@@ -269,7 +274,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
269
274
  reversed: boolean;
270
275
  } | undefined;
271
276
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
272
- export { renderToSvg, RefNameAutocomplete, SearchBox };
277
+ export { renderToSvg, RefNameAutocomplete, SearchBox, ZoomControls, LinearGenomeView, };
273
278
  export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
274
279
  export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
275
280
  export { default as ReactComponent } from './components/LinearGenomeView';
package/dist/LinearGenomeView/index.js CHANGED
@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
26
26
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
27
  };
28
28
  Object.defineProperty(exports, "__esModule", { value: true });
29
- exports.ReactComponent = exports.SearchBox = exports.RefNameAutocomplete = exports.renderToSvg = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
29
+ exports.ReactComponent = exports.LinearGenomeView = exports.ZoomControls = exports.SearchBox = exports.RefNameAutocomplete = exports.renderToSvg = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
30
30
  const react_1 = require("react");
31
31
  const configuration_1 = require("@jbrowse/core/configuration");
32
32
  const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
@@ -59,6 +59,12 @@ exports.RefNameAutocomplete = RefNameAutocomplete_1.default;
59
59
  const SearchBox_1 = __importDefault(require("./components/SearchBox"));
60
60
  exports.SearchBox = SearchBox_1.default;
61
61
  const ExportSvgDialog_1 = __importDefault(require("./components/ExportSvgDialog"));
62
+ const MiniControls_1 = __importDefault(require("./components/MiniControls"));
63
+ const Header_1 = __importDefault(require("./components/Header"));
64
+ const ZoomControls_1 = __importDefault(require("./components/ZoomControls"));
65
+ exports.ZoomControls = ZoomControls_1.default;
66
+ const LinearGenomeView_1 = __importDefault(require("./components/LinearGenomeView"));
67
+ exports.LinearGenomeView = LinearGenomeView_1.default;
62
68
  const SequenceSearchDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SequenceSearchDialog'))));
63
69
  function calculateVisibleLocStrings(contentBlocks) {
64
70
  if (!contentBlocks.length) {
@@ -147,6 +153,14 @@ function stateModelFactory(pluginManager) {
147
153
  },
148
154
  }))
149
155
  .views(self => ({
156
+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
157
+ MiniControlsComponent() {
158
+ return MiniControls_1.default;
159
+ },
160
+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
161
+ HeaderComponent() {
162
+ return Header_1.default;
163
+ },
150
164
  get assemblyErrors() {
151
165
  const { assemblyManager } = (0, util_1.getSession)(self);
152
166
  const { assemblyNames } = self;
@@ -518,6 +532,22 @@ function stateModelFactory(pluginManager) {
518
532
  setScaleFactor(factor) {
519
533
  self.scaleFactor = factor;
520
534
  },
535
+ // this "clears the view" and makes the view return to the import form
536
+ clearView() {
537
+ this.setDisplayedRegions([]);
538
+ self.tracks.clear();
539
+ // it is necessary to run these after setting displayed regions empty
540
+ // or else model.offsetPx gets set to Infinity and breaks
541
+ // mobx-state-tree snapshot
542
+ self.scrollTo(0);
543
+ self.zoomTo(10);
544
+ },
545
+ async exportSvg(opts = {}) {
546
+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
547
+ const html = await (0, LinearGenomeViewSvg_1.renderToSvg)(self, opts);
548
+ const blob = new Blob([html], { type: 'image/svg+xml' });
549
+ (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
550
+ },
521
551
  }))
522
552
  .actions(self => {
523
553
  let cancelLastAnimation = () => { };
@@ -572,6 +602,7 @@ function stateModelFactory(pluginManager) {
572
602
  .views(self => ({
573
603
  menuItems() {
574
604
  const { canShowCytobands, showCytobands } = self;
605
+ const session = (0, util_1.getSession)(self);
575
606
  const menuItems = [
576
607
  {
577
608
  label: 'Return to import form',
@@ -583,15 +614,19 @@ function stateModelFactory(pluginManager) {
583
614
  },
584
615
  icon: FolderOpen_1.default,
585
616
  },
586
- {
587
- label: 'Sequence search',
588
- onClick: () => {
589
- (0, util_1.getSession)(self).queueDialog(handleClose => [
590
- SequenceSearchDialog,
591
- { model: self, handleClose },
592
- ]);
593
- },
594
- },
617
+ ...((0, util_1.isSessionWithAddTracks)(session)
618
+ ? [
619
+ {
620
+ label: 'Sequence search',
621
+ onClick: () => {
622
+ (0, util_1.getSession)(self).queueDialog(handleClose => [
623
+ SequenceSearchDialog,
624
+ { model: self, handleClose },
625
+ ]);
626
+ },
627
+ },
628
+ ]
629
+ : []),
595
630
  {
596
631
  label: 'Export SVG',
597
632
  icon: PhotoCamera_1.default,
@@ -737,16 +772,6 @@ function stateModelFactory(pluginManager) {
737
772
  };
738
773
  })
739
774
  .actions(self => ({
740
- // this "clears the view" and makes the view return to the import form
741
- clearView() {
742
- self.setDisplayedRegions([]);
743
- self.tracks.clear();
744
- // it is necessary to run these after setting displayed regions empty
745
- // or else model.offsetPx gets set to Infinity and breaks
746
- // mobx-state-tree snapshot
747
- self.scrollTo(0);
748
- self.zoomTo(10);
749
- },
750
775
  setCoarseDynamicBlocks(blocks) {
751
776
  self.coarseDynamicBlocks = blocks.contentBlocks;
752
777
  self.coarseTotalBp = blocks.totalBp;
@@ -760,12 +785,6 @@ function stateModelFactory(pluginManager) {
760
785
  },
761
786
  }))
762
787
  .actions(self => ({
763
- async exportSvg(opts = {}) {
764
- // eslint-disable-next-line @typescript-eslint/no-explicit-any
765
- const html = await (0, LinearGenomeViewSvg_1.renderToSvg)(self, opts);
766
- const blob = new Blob([html], { type: 'image/svg+xml' });
767
- (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
768
- },
769
788
  /**
770
789
  * offset is the base-pair-offset in the displayed region, index is the index of the
771
790
  * displayed region in the linear genome view
@@ -1013,6 +1032,6 @@ function stateModelFactory(pluginManager) {
1013
1032
  }));
1014
1033
  }
1015
1034
  exports.stateModelFactory = stateModelFactory;
1016
- var LinearGenomeView_1 = require("./components/LinearGenomeView");
1017
- Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
1035
+ var LinearGenomeView_2 = require("./components/LinearGenomeView");
1036
+ Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_2).default; } });
1018
1037
  //# sourceMappingURL=index.js.map
package/dist/LinearGenomeView/index.js.map CHANGED
@@ -1 +1 @@
1
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